Yun Shi wrote:
Hi Justin and Mark,
Thank you very much for the reply.
I was using table 7 (Normal van der Waals Parameters) to calculate
non-bonded vdw interactions that are not between third neighbors, such
as CH1 carbons between different chains in a biomolecular system.
Anything wrong here?
I understand that it is the force that dictates the MD evolution, and I
calculated in this case as F = 12 * 9.85^2 / 1.5^13 = 5.98 kJ/mol/nm for
the repulsion term. The force from different directions on a atom in a
homogeneous system would cancel each other to some extend, but what
about the energy arises from this interaction? Would this considerably
affect the calculation of, say, binding energy of a ligand to a receptor
from thermodynamic integration or pulling simulation?
Check your units and the column headings of Table 7. Plugging in 9.85 as the
energy will give you a wildly inflated result. The C12 parameters listed are
actually square roots and listed as 10^-3. I think you will find the resulting
energies and forces are vastly smaller for a simple interaction between two atoms.
Besides, the GROMOS 53a6 paper used triple range scheme for calculations
of nonbonded interactions, and I guess it was rlist = 0.8 nm while rvdw
= rcoulomb = 1.4 nm. So is this considered to be accurate enough in
calculating free enthalpies of solvation since we know the interactions
between 0.8 and 1.4 nm were calculated every 5 steps?
There is no need to update the neighbor list every single step. Typically,
water is the fastest-diffusing molecule in the system, but it will generally not
have a dramatic displacement on the scale of 10 fs or so.
The paper also used reaction-field instead PME to account for long-range
electrostatic interactions. I heard some people argue that PME would be
more accurate and it seemed to be utilized more often even in gromacs
tutorials. So does this mean certain accuracy could be achieved by using
triple range scheme and reaction-field together because the errors they
incur respectively somehow cancel out each other?
PME is substantially more accurate. Using it also requires rlist=rcoulomb, so
the exact details of the Gromos96 derivation may be somewhat outdated. Typical
settings for Gromos96 would be something like:
rlist = 0.9
rcoulomb = 0.9
rvdw = 1.4
nstlist = 5
coulombtype = PME
Note that the value of rcoulomb and rlist can vary a bit as a consequence of
PME.
-Justin
Thanks a lot,
Yun Shi
On 04/08/11, "Justin A. Lemkul" <jalem...@vt.edu
<mailto:jalem...@vt.edu>> wrote:
>
>
> Yun Shi wrote:
> >Hi all,
> >
> >I am working with GROMOS 53a6 ff in GROMACS 4.5, and I assume a
Lennard-Jones interaction function was used for short-range vdw
interactions.
> >
> > From the reference paper /A Biomolecular Force Field Based on the
Free Enthalpy of Hydration and Solvation: The GROMOS Force-Field
Parameter Sets 53A5 and 53A6/, I found that for example,
> >
> >when rvdw = 1.5nm, the repulsion term of the interaction between two
CH1 type atoms (C12ij = 9.85^2) can be calculated as 9.850*9.850 /
(1.5^12) = 0.747786 kJ/mol. So I wonder if this value is considered to
be small enough to be ignored.
>
You should pay attention to the column headings in table 7 so that you
can compute the contribution correctly. However, the magnitude of the
energy of any particular interaction is not really of any concern. The
evolution of the system depends on the *forces*, and it is likely that
the sum of the forces on any atom from all its repulsion interactions
from atoms that are (say) 1.4nm to 1.5nm away is very close to zero,
except in highly non-homogeneous spatial distributions of particles. In
any case, the sum of that contribution will be much smaller than the
other contributions.
Mark
>
> >
> >In addition, it seems not until 5 nm does the dispersion term become
larger than the repulsion term in this case, so would turning on
Dispersion Correction between, say 1.5 to 5 nm introduce more errors
than turning it off?
> >
>
> You should use the cutoff described the authors of the force field,
in this case rvdw=1.4. Unless you can demonstrate that by using a
different value you can achieve superior results, stick with the
specifics of parameterization. I have never seen ill effects of setting
rvdw=1.4 and using dispersion correction with this force field.
>
> -Justin
>
> --
> ==============================
==========
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu <http://vt.edu/> | (540) 231-9080
<tel:%28540%29%20231-9080>
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
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========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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